The invention discloses a carbon quantum dot sensor with copper ion and cysteine recognition functions, a preparation method and application thereof. The carbon quantum dot sensor is prepared by the following steps: taking citric acid and ethylene diamine as raw materials, adopting a microwave method to synthesize a carbon quantum dot containing carboxyl on the surface, then taking 2-bromoethylamine and 1,4,8,11-tetraazacyclotetradecane as surface functionalizing reagents, and utilizing a surface grafting technology. The carbon quantum dot sensor is good in dispersity in water, and can be used for double-selectivity fluorescence detection to the copper ion and cysteine. Compared with the existing detection technology, the carbon quantum dot sensor disclosed by the invention can detect trace of copper ion and cysteine in a pure water medium with high sensitivity and high selectivity, is simple in synthetic route, convenient to use, and suitable for large-scale synthesis and actual application in production, and has the enormous application prospect in the fields such as biology and environment detection.